PayPal’s bid for the digital wallet looks strong

FORTUNE — As long as the Internet has been a venue for commerce, some companies have dreamed of making electronic cash as seamless and intuitive to use as possible: no cash or coins, no check-writing, no typing in or storing credit card numbers. Thanks to the rise of the cloud and the popularity of smarphones, that idea is becoming real.

As a result, the names of companies working to create a so-called digital wallet is growing: startups like Square, big-name companies like eBay EBAY, Google GOOG and Apple AAPL or financial services giants like Visa V and MasterCard MA – each hoping for a key role in what could in coming years become a lucrative market.

No company has been working longer at this goal than PayPal. Back when people spoke less of the cloud and more about grid computing, and when mobile phones were too big to fit comfortably inside a pocket, PayPal was laying the foundation for a global e-payment system – working through regulatory processes in hundreds of countries, grappling with myriad forms of online fraud and fielding customer complaints.

Today, PayPal works with 9 million merchants and 106 million active customers. And over the past couple of years, the eBay EBAY unit has been quietly assembling a strategy to create a digital wallet for those customers, and potentially many more. But it means improving on offerings from competitors, some of which have large customer bases and ample cash reserves.

It also means placing bets on which standards consumers and merchants will embrace. Will Square-like dongles become an everyday accessory in retail? Or will near-field communications overcome security concerns and become the norm? Will credit- and debit- accounts continue to play a central role? And most importantly, which brands will emerge as the most trusted consumer interface to mobile payments?

Slowly, PayPal’s strategy is becoming clearer. After buying startups such as BillMeLater, shopping-engine Milo and app developers WHERE and Redlaser, PayPal has begun rolling out new features – most recently its PayPal Here service. Announced last week, PayPal Here was widely seen as a competitor of Square, the startup noted for the dongle that plugs into smartphones for on-the-spot payments in stores and restaurants.

Square is catching on with many retailers. PayPal says it saw $4 billion in mobile payments in 2011 and that it expects to top $7 billion this year. But Square also says it processed $4 billion in payments last year, largely from small brick-and-mortar retailers that PayPal has tended to overlook.

Both companies are quickly moving beyond the simple dongle. Square offers Card Case, an iPhone app that lets people pay Square’s retail clients without swiping a plastic card. PayPal Here also allows wireless payments with participating retailers. Through a partnership with Card.io, PayPal Here can also take a photo of a credit card instead of using a dongle.

But PayPal Here is just one part of what the company is planning in what is shaping up to be an ambitious strategy. Over the past two months, PayPal has rolled out its payment technology to nearly 2,000 Home Depot stores as an alternative to credit cards. It’s partnered with Ingenico and AJB Software Designs to create an in-store payment system that can be quickly rolled out to other large chains.

It’s too early to tell if PayPal Here will become more than a payment method for people who left their wallets at home. The company’s $7 billion estimate for 2012 mobile payments doesn’t include such point-of-sale transactions. PayPal charges merchants a 2.7% transaction fee, which is roughly equal to Square’s 2.75% and may offer merchants an incentive to push for PayPal if it’s cheaper than credit card transactions.

But as important as smartphones may become in handling payments, PayPal is aiming well beyond them, offering a method of payment on PCs as well as the ubiquitous point-of-service terminals at brick-and-mortar cash registers. Ebay is also sure to integrate PayPal deeply into its X.Commerce initiative, a commerce platform announced last fall for online as well as offline retailers.

As PayPal’s strategy comes slowly into focus, it’s clear the company is thinking broadly – positioning its service in as many commercial venues as possible – and designing an interface that appeals to merchants and consumers alike. Anuj Nayar, PayPal’s director of communications, says the company will roll out even more changes starting this month that “marks the beginning of fundamental change in what PayPal means to customers.”

Until now, for many PayPal customers, the service has simply been one of multiple ways to pay online, most often seen as an alternative to credit cards. After years of planning, the company may finally be worming its way into our wallets, becoming as commonplace as cash once was. The rest of this year should show whether PayPal can deliver on that promise.